title: WT_TA100_3

city: Hefei

first: Wen

last: Pan

address: 443 Huangshan Road

department: School of Life Sciences, USTC Life Sciences and Medicine

institute: University of Science and Technology of China

data_processing:
The reads were aligned to the mouse mm10 reference genome using STAR aligner (v.2.5.3a) with default parameters and quantified.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Intestinal organoid

extract_protocol:
Total RNAs were extracted from organoid using TRIzol Reagent (Tiangen, cat. DP424）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: Intestinal organoid

value: WT


title: WT_TA100_2

status: Public on May 25 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: Mouse 2, Tumour, Day 8 IT, EYFP+

city: Cambridge

first: James

last: Thaventhiran

address: Tennis Court Road

country: United Kingdom

institute: MRC Toxicology Unit

description: SMARTer Mouse TCR α/β Profiling kit (Takara Bio USA)

data_processing:
Sequencing data were analysed and clonotypes were called using MiXCR v4.4.2 with recommended settings for SMARTer Mouse TCR α/β Profiling kit (analyze takara-mouse-rna-tcr-smarter).
Cells were grouped by their TCR β sequences, and the top 200 largest EYFP+ clonal populations (by frequency in the 10 tumour) from each mice were used for subsequent analysis. Sequences matching public repertoires were removed (Immune Epitope Database).
Assembly: mm10
Supplementary files format and content: Tab-separated values files

source_name: Tumour

extract_protocol:
Freshly collected cells were sorted into Buffer RLT Plus buffer (Qiagen) with 20mM DTT. Lysate was vortexed for 1 min and stored at −80 °C for subsequent analysis. Total RNA was then extracted with RNeasy Plus Micro Kit as per manufacturers recommendations. RNA QC with Tapestation High Sensitivity RNA showed RIN values above 9.8 for all samples.
Samples were prepared withTakara SMARTer Mouse TCR alpha-beta Profiling Kit for 96 samples as per manufacturers recommendations.

value: Tumour

tag: cell type

value: EYFP+ T cells

value: 8 days after intratumoral tamoxifen

tag: library type

value: Other


title: WT_TA100_1


title: Mouse 1, dLN, Day 8 IT, EYFP-

source_name: Draining lymph node

value: Draining lymph node

value: EYFP- T cells


title: Patient, biol rep 2

city: New Delhi

first: Vibha

last: Taneja

state: Delhi

address: Rajinder Nagar

department: Research

country: India

institute: Sir Ganga Ram Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimgalore (Phred score threshold of 20)
Trimmed sequence reads were mapped to GRCh38 using STAR aligner.
Read count extraction was done using Salmon and normalization were performed using Voom.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

source_name: Blood

extract_protocol:
Peripheral blood was drawn in EDTA vials. Peripheral blood mononuclear cells (PBMCs) were separated by density gradient centrifugation on Histopaque-1077. RNA was isolated from PBMCs using RNAzol according to the manufacturer’s protocol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Blood

value: Peripheral blood mononuclear cells

value: Juvenile Amyotrophic Lateral Sclerosis


title: WT_DMSO_3

value: DMSO


title: WT_DMSO_2


title: Mouse 1, Tumour, Day 8 IT, EYFP-


title: Mouse 1, Tumour, Day 8 IT, EYFP+


title: Dd_L1_rep4

city: Wuhan

first: Dadong

last: Dai

state: Hubei

address: 1st street Shizishan

department: Department of Life science and technology

institute: Huazhong Agricultural University

data_processing:
sequence read was trimmed for adaptor sequence/low-quality using fastp (v0.20.1) software
read count extraction and normalization were performed using RSEM29 (v1.2.28)
Assembly: The genome used in this study was sequenced and assembled in our own laboratory and has not yet been published.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Ditylenchus destructor

source_name: whole organism

extract_protocol:
RNA was harvested by treating eggs with lysis buffer. Details can refer to smart-seq2 peotocols.
RNA libraries for RNA-seq were prepared using Smart-seq2 protocols.

value: whole organism


title: WT_DMSO_1


title: Dd_L1_rep5


title: Mouse 1, dLN, Day 8 IT, EYFP+


title: Mouse D, ndLN, Day 8 IP, EYFP+

source_name: Non-draining lymph node

value: Non-draining lymph node

value: 8 days after intraperitoneal tamoxifen


title: Mouse D, dLN, Day 8 IP, EYFP-


title: Dd_L1_rep2


title: Mouse 2, Tumour, Day 8 IT, EYFP-


title: Patient, biol rep 1


title: Dd_L1_rep3


title: Dd_L1_rep1


title: Mouse D, Spleen, Day 8 IP, EYFP-

source_name: Spleen

value: Spleen


title: Mouse D, dLN, Day 8 IP, EYFP+


title: HUVEC, ATAC-Seq, TNF-alpha stimulated, biological replicate 2 (T2)

city: Unionville

first: Haibo

last: Liu

state: CT

address: 164 Plantation St

department: MCCB

country: USA

institute: UMass Chan

library_source: genomic

data_processing:
Paired-end raw reads were trimmed using Trimmomatic (v0.32) to remove adapter sequences: java -jar  /share/pkg/trimmomatic/0.32/trimmomatic-0.32.jar  PE -threads 8 \           -phred33 ${R1[$i]} ${R2[$i]} \           $out/${name[$i]}.R1Ptrim.fastq.gz  $out/${name[$i]}.R1Utrim.fastq.gz \           $out/${name[$i]}.R2Ptrim.fastq.gz  $out/${name[$i]}.R2Utrim.fastq.gz  \           ILLUMINACLIP:${adapter}:2:25:7:1:true  TRAILING:3 \           SLIDINGWINDOW:4:15  TRAILING:3 MINLEN:25
The resulting paired-end reads were mapped to the human reference genome using bwa mem (v0.7.17-r1188): bwa mem -M -t 8 -R @RG\tID:C1\tPL:ILLUMINA\tSM:C1\tPU:unit1\tLB:C1 /home/haibo.liu-umw/mccb-umw/shared/genome/homo.sapiens/T2T-CHM13v2.0/T2T-CHM13v2.0_genomic.fa trimmed.data/C1.R1Ptrim.fastq.gz trimmed.data/C1.R2Ptrim.fastq.gz
The resulting BAM files were coordinate-sorted using SAMtools (v1.16.1)
Duplicates were removed using MarkDuplicates (v2.27.5) of the Picard Tools. Reads aligned to the mitochondrial genome, or with mapping quality < 20,  discordantly mapped, insert size out of  the range of [38, 2000] were removed using SAMtools (v1.16.1) and an AWK script: # Non-mitochondrial chromosome names:     chromosomes=($(samtools view -H ${bam[$i]} | grep '^@SQ' | perl -n -e 's{.+?SN:([^\t]+).+}{$1}; if ($_ ne "MT\n" && $_ ne "chrM\n") {print}'))      # Only output non-mitochondiral reads, prperly mapped, insert size in the range of [38, 2000], mapq >= 20     #samtools index $bam       samtools view -h -@ 8  ${bam[$i]}  ${chromosomes[@]} | awk 'BEGIN{FS=OFS="\t"} \     function abs(v) {return v < 0 ? -v : v}; \     /^@/ || ($7 == "=" && ($2 == 99 || $2 == 147 || $2 == 83 || $2 == 163) && abs($9) <= 2000 && abs($9) >= 38 && $5 >= 20 ) {print}' |samtools view -bh - \     > $out/${name[$i]}.filtered.bam.
The filtered BAM files were converted to BigWig files to get normalized genome coverage signal using Deeptools (v3.5.1): bamCoverage -b ${bams[$i]} \           -o $out/${names[$i]}.bigwig \           --blackListFileName  $blacklist \           --outFileFormat bigwig \           --numberOfProcessors 8\           --effectiveGenomeSize $gsize  \           --normalizeUsing RPGC  \           --smoothLength  60 \           --binSize 20 \           --extendReads
Assembly: T2T-CHM13v2.0 from Ensembl rapid release
Supplementary files format and content: BigWig files, genome wide read coverage normalized using the RPGC method.

molecule: genomic DNA

source_name: HUVEC

growth_protocol: Cell culture and treatment. Human umbilical vein endothelial cells (HUVECs; #PCS100010) were purchased from ATCC and cultured in endothelial cell growth basal medium-2 containing bullet kit growth factor supplements (EBM-2 [endothelial cell growth basal medium-2]; Lonza), 5% fetal bovine serum, 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mmol/L L-glutamine (Invitrogen) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
HUVEC cells were grown in dishes, cryopreserved in 1ml of media with DMSO containing 0.5-1.5x10^6 cells. The experiment was done in biological duplicate, paired with RNA-seq experiment. The ATAC-seq experiments have been conducted by the Diagenode ATAC-seq Profiling service (Diagenode Cat# G02060000).  Transposition. Cell viability and cell counting were evaluated by visualization under the microscope (AE2000; Matic). 200,000 cells were centrifuged at 500g before proceeding with the nuclei isolation and transposition reaction using the ATAC-seq Kit from Diagenode (Diagenode Cat #C01080002). According to the results of the nuclei isolation optimization, the Tween20/Igepal concentration in Lysis buffer 1 used was 0,1% with an incubation time of 3 minutes. 50,000 counted nuclei were transferred to a new tube and were centrifuged at 500g before proceeding with the transposition reaction. Isolated nuclei were lysed and transposed for 30 minutes at 37°C using the prokaryotic Tn5 transposase system (Nextera DNA library kit, Illumina, FC-121–1030). Transposed DNA was then purified on Diapure columns (Diagenode Cat# C03040001).  Transposition. Cell viability and cell counting were evaluated by visualization under the microscope (AE2000; Matic). 200,000 cells were centrifuged at 500g before proceeding with the nuclei isolation and transposition reaction using the ATAC-seq Kit from Diagenode (Diagenode Cat #C01080002). According to the results of the nuclei isolation optimization, the Tween20/Igepal concentration in Lysis buffer 1 used was 0,1% with an incubation time of 3 minutes. 50,000 counted nuclei were transferred to a new tube and were centrifuged at 500g before proceeding with the transposition reaction. Isolated nuclei were lysed and transposed for 30 minutes at 37°C using the prokaryotic Tn5 transposase system (Nextera DNA library kit, Illumina, FC-121–1030). Transposed DNA was then purified on Diapure columns (Diagenode Cat# C03040001).
Library preparation. Libraries were prepared from purified transposed DNA using NEBNext High-Fidelity PCR MasterMix (NEB, M0541) and Illumina indexing primers. The number of library amplification cycles was determined by qPCR analysis using NEBNext High-Fidelity PCR MasterMix (NEB, M0541) on LightCycler® 96 System (Roche). After their amplification, the libraries were size selected and purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally, their fragment size was analyzed by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). Libraries were pooled and sequenced on an Illumina NovaSeq6000 in a 2 × 50-bp, paired-end mode.

treatment_protocol: Cells (passages 3 and 4) were treated were either left untreated (control), exposed for 6 hours to 10ng/ml TNF-alpha (210-TA-020 (R&Dsystems) or treated for 2 hours with heat stress (39ºC) in water bath.

tag: cell line

value: HUVEC

value: vascular endothelial

value: TNF-alpha


title: HUVEC, ATAC-Seq, 39 °C heat stress for 2 hours, biological replicate 2 (HS2)

value: heat stress


title: HUVEC, ATAC-Seq, TNF-alpha stimulated, biological replicate 1 (T1)


title: HUVEC, ATAC-Seq, 39 °C heat stress for 2 hours, biological replicate 1 (HS1)


title: Dd_Moving_rep5


title: 𝚫rrpA/B_48_3

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

description:
50-bp single read sequencing
rrpAB_48h_R3

data_processing:
The sequencing results were analyzed with Unitas (https://doi.org/10.1186/s12864-017-4031-9) using default parameters.
A. fumigatus nuclear tRNAs were referenced from GtRNAdb, mitochondrial tRNAs were scanned from the mitochondrial genome using the 27 tRNAs predicted by tRNAscan-SE. All analyses were performed using “R” version 4.3.1 (2023-06-16) and Rstudio (2022-02-02), an integrated development environment (IDE) for R.
Assembly: Aspergillus fumigatus A1163 ASM15014v1
Supplementary files format and content: A single csv file (sRNA_processed) contains the abundance of each target from each sample replicate.

organism: Aspergillus fumigatus

source_name: mycelium

growth_protocol: A. fumigatus was grown on Aspergillus minimal medium (AMM) agar plates (70 mM NaNO3, 11.2 mM KH2PO4, 7 mM KCl, 2 mM MgSO4, 1% (w/v) glucose and 1 μl/ml trace element solution (pH 6.5)). The trace element solution was composed of 1 g FeSO4 • 7 H2O, 8.8 g ZnSO4 • 7 H2O, 0.4 g CuSO4 • 5 H2O, 0.15 g MnSO4 • H2O, 0.1 g NaB4O7 • 10 H2O, 0.05 g (NH4)6Mo7O24 • 4 H2O, and ultra-filtrated water to 1000 ml. Spores were harvested after 5 days with 10 ml of sterile distilled water using a T-shaped inoculation spreader and spore suspensions were filtered through a 30-µm cell strainer (MACS, Miltenyi Biotec GmbH, Germany) to exclude mycelium.

extract_protocol:
Total RNA was isolated from three biological replicates of CEA17ΔakuBKU80, ΔppdA/B, ΔdclA/B, and ΔrrpA/B knockout strains from conidia, 24-h-, and 48-h-old mycelium. For A. fumigatus conidia, the spores were first homogenized in a bead beater (0.5 mm beads; FastPrep-24, MP Biomedicals) in Trizol. Fungal mycelium was collected from liquid culture using Miracloth (Millipore) and disrupted in liquid nitrogen using a precooled mortar and pestle. Roughly 0.5 g of homogenized mycelium was transferred into a 2-ml Eppendorf tube. 800 µl TRIzol was added to the ground mycelia and vortexed vigorously. Tubes were frozen briefly for 5 sec in liquid nitrogen and allowed to thaw on ice. To all samples, chloroform was added to the fungal samples in TRIzol, vortexed, and centrifugated for 5 min at 4°C at full speed. The aqueous upper phase was transferred to a fresh 2-ml tube without disturbing the interphase. RNA extraction from aqueous phase was done with 1 volume of phenol/chloroform/isoamyl alcohol (25:24:1, v/v). Brief vortexing preceded centrifugation for 5 min at 4°C. RNA was precipitated using 400 µl isopropanol for 20 min, followed by pelleting by centrifugation for 20 min at 4°C. The pellet was washed with 700 µl 70% ethanol and air dried at 37°C for 5 min prior to resuspension in RNase free water. The RNA isolation was followed by a DNase treatment using 2 units of TURBO DNase (Thermo Fisher) per 10 µg RNA for 30 min at 37°C in 100 µl total volume. Total RNA was then collected using the RNA Clean and Concentrator-25 kit (Zymo Research) according to the manufacturer’s instructions. These samples were collected simultaneously as matched samples with those reported in GEO Series GSE223618.
Libraries were constructed by Novogene. According to the manufacturer, 3' and 5' adaptors were ligated to 3' and 5' ends of small RNA, repsectively. Then the first strand cDNA was synthesized after hybridization with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18-40 bp were ready for sequencing with SE50.

value: mycelium

value: CEA17 delta_akuB::KU113

tag: growth condition

value: Aspergillus minimal media agar plates

value: {delta}rrpA/B


title: HUVEC, ATAC-Seq, control, biological replicate 2 (C2)

value: control


title: HUVEC, ATAC-Seq, control, biological replicate 1 (C1)


title: Mouse D, Spleen, Day 8 IP, EYFP+

value: EYFP+ T cells

value: Other


title: Dd_Moving_rep4


title: 𝚫rrpA/B_48_2

description:
50-bp single read sequencing
rrpAB_48h_R2

value: CEA17 delta_akuB::KU112


title: Mouse D, ndLN, Day 8 IP, EYFP-

value: EYFP- T cells


title: Mouse D, Tumour, Day 8 IP, EYFP-

value: Tumour


title: Dd_Moving_rep3

value: whole organism


title: HUVEC, TNF-alpha stimulated, biological replicate 3 (T3)

data_processing:
Paired-end reads were mapped to the human reference genome using STAR (v2.7.10a): STAR   --runThreadN 8   --genomeDir /home/haibo.liu-umw/mccb-umw/shared/genome/homo.sapiens/T2T-CHM13v2.0/T2T-CHM13v2.0.sjdboverhang149   --readFilesIn data/C1_R1.fq.gz   data/C1_R2.fq.gz      --readFilesCommand zcat      --limitSjdbInsertNsj 2000000   --outFileNamePrefix results/003.STAR.out//C1   --outSAMtype BAM   Unsorted      --outFilterType BySJout   --outFilterMultimapNmax 10   --outFilterScoreMinOverLread 0.3   --outFilterMatchNminOverLread 0.3   --outFilterMismatchNmax 999   --outFilterMismatchNoverReadLmax 0.04   --seedSearchStartLmax 50   --seedSearchStartLmaxOverLread 0.15   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1   --twopassMode Basic
Expression quantification using featureCounts (v1.6.2): featureCounts -p -Q 255 -s 0 -F GTF -J -g gene_id -G /home/haibo.liu-umw/mccb-umw/shared/genome/homo.sapiens/T2T-CHM13v2.0/T2T-CHM13v2.0_genomic.fa -t exon -T 8 -a /home/haibo.liu-umw/mccb-umw/shared/genome/homo.sapiens/T2T-CHM13v2.0/T2T-CHM13v2.0-2022_07-Ensembl.genes.gtf -o results/004.featureCount.out/Ana.RNAseq.exon.uniqmap.2 results/008.samtools.sort.out/C1.sorted.bam results/008.samtools.sort.out/C2.sorted.bam results/008.samtools.sort.out/C3.sorted.bam results/008.samtools.sort.out/HS1.sorted.bam results/008.samtools.sort.out/HS2.sorted.bam results/008.samtools.sort.out/HS3.sorted.bam results/008.samtools.sort.out/T1.sorted.bam results/008.samtools.sort.out/T2.sorted.bam results/008.samtools.sort.out/T3.sorted.bam
Based on the featureCounts output from last step, genes with zero counts were excluded from the GTF file to get a filtered GTF file.
Expression quantification using featureCounts (v1.6.2) again using the same command except the filtered GTF file was used.
Assembly: T2T-CHM13v2.0 from Ensembl rapid release along its genome annotation file: T2T-CHM13v2.0/T2T-CHM13v2.0-2022_07-Ensembl.genes.gtf
Supplementary files format and content: Tab-delimited (.tsv) gene-by-sample count table

extract_protocol:
HUVEC cells were grown in dishes, either left untreated or subjected to inflammatory stressor TNF alpha for 6hrs or febrile-mimicking heat stress for 2hrs and cryopreserved in 1ml of freezing media containing more than 0.4x10^6 cells. The experiments were done in biological triplicate. RNA-seq was done by Diagenode Inc. Specifically, nine cryopreserved samples were used for total RNA extraction using the Qiagen RNeasy mini kit (Qiagen Cat #74104). The RNA-seq experiment has been conducted by RNA-seq services (Diagenode Cat# G02030000). RNAs have been firstly quantified using Qubit™ RNA HS Assay Kit RNA HS Assay Kit (Thermo Fisher Scientific, Cat# Q32852). The RNA integrity was assessed using a Bioanalyzer, RNA 6000 Pico kit (Agilent  Cat# 5067-1513,) on a 2100 Bioanalyzer system (Agilent). The samples with RINs above 7 were used for RNA-seq.
Library preparation has been done with 250ng of input RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) followed by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext® Multiplex Oligos for Illumina® Index Primers Set 1 (NEB# E6440). The generated DNA libraries were purified using Agencourt® AMPure® XP (Beckman Coulter). Purified libraries were quantified, and their size was assessed with QIAxcel (Qiagen). The library pool was then sequenced on NovaSeq paired-end 50bp.


title: 𝚫rrpA/B_48_1

description:
50-bp single read sequencing
rrpAB_48h_R1

value: CEA17 delta_akuB::KU111


title: Dd_Moving_rep2


title: 𝚫ppdA/B_48_3

description:
50-bp single read sequencing
ppdAB_48h_R3

value: CEA17 delta_akuB::KU110

value: {delta}ppdA/B


title: HUVEC, TNF-alpha stimulated, biological replicate 1 (T1)

value: HUVEC

value: vascular endothelial


title: Mouse C, ndLN, Day 8 IP, EYFP-

value: Non-draining lymph node

value: 8 days after intraperitoneal tamoxifen


title: Dd_Moving_rep1


title: 𝚫ppdA/B_48_2

description:
50-bp single read sequencing
ppdAB_48h_R2

value: mycelium

value: CEA17 delta_akuB::KU109


title: Dd_2-fold_rep5


title: HUVEC, 39 °C heat stress for 2 hours, biological replicate 3 (HS3)

value: heat stress


title: Mouse C, ndLN, Day 8 IP, EYFP+


title: HUVEC, 39 °C heat stress for 2 hours, biological replicate 2 (HS2)


title: Dd_2-fold_rep4


title: Dd_2-fold_rep3


title: Mouse C, dLN, Day 8 IP, EYFP+

value: Draining lymph node


title: HUVEC, control, biological replicate 3 (C3)

value: control


title: Mouse C, Spleen, Day 8 IP, EYFP-

value: Spleen

value: Other


title: 𝚫dclA/B_48_2

description:
50-bp single read sequencing
dclAB_48h_R2

value: CEA17 delta_akuB::KU106

value: Aspergillus minimal media agar plates

value: {delta}dclA/B


title: Mouse C, Spleen, Day 8 IP, EYFP+

value: EYFP+ T cells


title: Dd_2-fold_rep2

value: whole organism


title: Mouse D, Tumour, Day 8 IP, EYFP+

value: Tumour


title: 𝚫dclA/B_48_1

description:
50-bp single read sequencing
dclAB_48h_R1

value: CEA17 delta_akuB::KU105


title: HUVEC, TNF-alpha stimulated, biological replicate 2 (T2)

value: HUVEC

value: vascular endothelial

value: TNF-alpha


title: Wild-type_48_3

description:
50-bp single read sequencing
CEA17_48h_R3

value: mycelium

value: CEA17 delta_akuB::KU104

value: wild type


title: HUVEC, control, biological replicate 2 (C2)


title: Mouse C, Tumour, Day 8 IP, EYFP-

value: EYFP- T cells

value: 8 days after intraperitoneal tamoxifen


title: Dd_2-fold_rep1


title: HUVEC, control, biological replicate 1 (C1)

value: control


title: Wild-type_48_2

description:
50-bp single read sequencing
CEA17_48h_R2

value: CEA17 delta_akuB::KU103


title: Dd_1.5-fold_rep5


title: 𝚫ppdA/B_48_1

description:
50-bp single read sequencing
ppdAB_48h_R1

value: CEA17 delta_akuB::KU108

value: {delta}ppdA/B


title: Mouse C, Tumour, Day 8 IP, EYFP+

value: Other


title: Mouse C, dLN, Day 8 IP, EYFP-

value: Draining lymph node


title: 𝚫dclA/B_48_3

description:
50-bp single read sequencing
dclAB_48h_R3

value: CEA17 delta_akuB::KU107

value: Aspergillus minimal media agar plates

value: {delta}dclA/B


title: Bewo siVGLL1

city: Houston

first: Heather

last: Sonnemann

address: 7455 Fannin St

institute: MD Anderson Cancer Center

data_processing:
Sequence reads were analyzed with the STAR alignment–DESeq2 software pipeline
Assembly: hg_38
Supplementary files format and content: tab-separated values contain counts for each sample
Supplementary files format and content: tab-separated values contain TPM values for each sample

source_name: Placenta

growth_protocol: PANC10.05 cells were maintained  in RPMI with 10% FBS. BT20 cells were maintained in EMEM contailing 10% FBS. Bewo cells were maintained in Ham's F-12K medium with 10% FBS. All cells were maintained in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was isolated from the cells after the 48hour knockdown using RNAeasy Plus mini kit (Qiagen, cat#74134). 500ng of total RNA was used for construction of sequencing library
RNA libraries for RNA-seq were prepared using Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594)

treatment_protocol: The cells at 60-80% confluency were used for transfection with siVGLL1 (ThermoFisher Scientific, cat#4392420 s28152) or siScramble control (ThermoFisher Scientific, cat#4390846) for 48 hours.

value: Placenta

value: Bewo

value: Epithelial

value: VGLL1 knockdown

value: siRNA VGLL1


title: Wild-type_48_1

description:
50-bp single read sequencing
CEA17_48h_R1

value: mycelium

value: CEA17 delta_akuB::KU102

value: wild type


title: WT Small pre-B 1

status: Public on May 31 2024

city: Melbourne

first: Zhoujie

last: Ding

state: VIC

address: 89 Commercial Road

country: Australia

institute: Monash University

data_processing:
Raw FASTQ files were trimmed with trimmomatic using NexteraPE-PE.fa
Trimmed FASTQ files were aligned to UCSC mm10 genome. Duplicated, mitochondrial and low quality reads were removed.
BAM files were shifted to account for Tn5 cutting sites before MACS2 peak calling (-f BED -q 0.01 --nomodel --shift -75 --extsize 150).
Bigwig tracks were generated with deepTools with RPGC normalization.
Differential analysis was performed using Diffbind (DESeq2 method), and significantly differential regions were filtered by FDR < 0.05.
Assembly: mm10
Supplementary files format and content: bigwig, signal track
Supplementary files format and content: narrowPeak, peaks

source_name: Bone marrow

extract_protocol:
Cells were pelleted at 500xg for 10 minutes at 4 degree. Tagmentation reaction containing 0.02% Digtonin, 0.1% Tween-20, Tagment DNA Enzyme 1, Tagment DNA Buffer and moleular grade H2O in 25 uL volume per sample was added to each of the cell pellet. Tagmentation was performed at 37 degrees for 60min followedd by 30 min digestion with Proteinase-K
DNA samples were first purified by SPRI bead size selection. Libraries were amplified using Kapa HiFi HotStart Polymerase Ready Mix in 50 uL volume with indexing primers. A post-PCR SPRI bead clean up was performed to purify the libraries.

value: Bone marrow

value: lymphoid progenitor cells

value: WT


title: Bewo siScramble

value: siScramble


title: Mouse B, ndLN, Day 8 IP, EYFP-

value: Non-draining lymph node

value: EYFP- T cells

value: 8 days after intraperitoneal tamoxifen

value: Other


title: HUVEC, 39 °C heat stress for 2 hours, biological replicate 1 (HS1)

value: HUVEC

value: vascular endothelial

value: heat stress


title: Dd_1.5-fold_rep4

value: whole organism


title: Dd_1.5-fold_rep3


title: 𝚫rrpA/B_24_3

description:
50-bp single read sequencing
rrpAB_24h_R3

value: CEA17 delta_akuB::KU101

value: Aspergillus minimal media agar plates

value: {delta}rrpA/B


title: Mouse B, ndLN, Day 8 IP, EYFP+

value: EYFP+ T cells


title: PANC10.05 siVGLL1

source_name: Panceas

value: Pancreas

value: Epithelial

value: VGLL1 knockdown

value: siRNA VGLL1


title: Dd_1.5-fold_rep2


title: 𝚫rrpA/B_24_2

description:
50-bp single read sequencing
rrpAB_24h_R2

value: mycelium

value: CEA17 delta_akuB::KU100


title: Mouse B, dLN, Day 8 IP, EYFP-

value: Draining lymph node

value: EYFP- T cells


title: PANC10.05 siScramble

source_name: Pancreas

value: WT

value: siScramble


title: 𝚫rrpA/B_24_1

description:
50-bp single read sequencing
rrpAB_24h_R1

value: CEA17 delta_akuB::KU99


title: 𝚫ppdA/B_24_3

description:
50-bp single read sequencing
ppdAB_24h_R3

value: CEA17 delta_akuB::KU98

value: {delta}ppdA/B


title: Mouse B, dLN, Day 8 IP, EYFP+

description: SMARTer Mouse TCR α/β Profiling kit (Takara Bio USA)

value: 8 days after intraperitoneal tamoxifen

value: Other


title: Dd_Comma_rep5

value: whole organism


title: BT20 siVGLL1

source_name: Breast

value: Breast


title: BT20 siScramble


title: Dd_1.5-fold_rep1


title: Mouse B, Spleen, Day 8 IP, EYFP-

value: Spleen


title: Mouse B, Spleen, Day 8 IP, EYFP+

value: EYFP+ T cells


title: Bewo VGLL1

data_processing:
Processing of Illumina base-call data and demultiplexing was performed using bcl2fastq2 (v2.20)
Reads were aligned to the human genome (hg38) using the BWA algorithm
Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library and assigned to 32-nt bins along the genome
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7
Assembly: hg_38
Supplementary files format and content: BigWig

extract_protocol:
the cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer and disrupted with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat#53051)
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara)

value: Placenta

value: Bewo

value: Epithelial

tag: chip antibody

value: VGLL1 (Protein Tech, cat#10124-2-AP)


title: Dd_Comma_rep3


title: 𝚫ppdA/B_24_2

description:
50-bp single read sequencing
ppdAB_24h_R2

value: mycelium

value: CEA17 delta_akuB::KU97

value: Aspergillus minimal media agar plates


title: 𝚫ppdA/B_24_1

description:
50-bp single read sequencing
ppdAB_24h_R1

value: CEA17 delta_akuB::KU96


title: Mouse B, Tumour, Day 8 IP, EYFP-

value: Tumour

value: EYFP- T cells


title: Dd_Comma_rep4


title: Dd_Comma_rep2


title: Mouse B, Tumour, Day 8 IP, EYFP+


title: Dd_Comma_rep1


title: 𝚫dclA/B_24_2

description:
50-bp single read sequencing
dclAB_24h_R2

value: CEA17 delta_akuB::KU94

value: {delta}dclA/B


title: Bewo input

value: WT


title: 𝚫dclA/B_24_3

description:
50-bp single read sequencing
dclAB_24h_R3

value: CEA17 delta_akuB::KU95


title: PANC10.05 VGLL1

value: Pancreas


title: Dd_64-78cell_rep5

value: whole organism


title: PANC10.05 input


title: Mouse A, ndLN, Day 8 IP, EYFP-

value: Non-draining lymph node

value: 8 days after intraperitoneal tamoxifen

value: Other


title: Mouse A, ndLN, Day 8 IP, EYFP+

value: EYFP+ T cells


title: 𝚫dclA/B_24_1

description:
50-bp single read sequencing
dclAB_24h_R1

value: CEA17 delta_akuB::KU93


title: Dd_64-78cell_rep4


title: BT20 VGLL1

value: Breast

value: Epithelial

value: VGLL1 (Protein Tech, cat#10124-2-AP)


title: Mouse A, dLN, Day 8 IP, EYFP-

value: Draining lymph node


title: Wild-type_24_3

description:
50-bp single read sequencing
CEA17_24h_R3

value: mycelium

value: CEA17 delta_akuB::KU92

value: Aspergillus minimal media agar plates

value: wild type


title: BT20 input

value: WT


title: Wild-type_24_2

description:
50-bp single read sequencing
CEA17_24h_R2

value: CEA17 delta_akuB::KU91


title: Mouse A, dLN, Day 8 IP, EYFP+


title: Sample 16

city: changchun

first: Gen

last: Qin

address: renmin street 5625

department: Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization

institute: Changchun Institute of Applied Chemistry, Chinese Academy of Sciences

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg19
Supplementary files format and content: files include RPKM values for each Sample
Supplementary files format and content: bigWig

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: HeLa cells

value: MYC inhibition

value: dCas9-nucleolin + sgR-5


title: Dd_24-44cell_rep4

value: whole organism


title: Wild-type_24_1

description:
50-bp single read sequencing
CEA17_24h_R1

value: CEA17 delta_akuB::KU90


title: Dd_24-44cell_rep5


title: Dd_64-78cell_rep1


title: Sample 13

value: dCas9-nucleolin + sgR-Ctrl


title: Mouse A, Spleen, Day 8 IP, EYFP+

value: Spleen

value: EYFP+ T cells

value: 8 days after intraperitoneal tamoxifen

value: Other


title: Sample 14


title: Sample 15


title: 𝚫rrpA/B_conidia_2

description:
50-bp single read sequencing
rrpAB_conidia_R2

source_name: conidia

value: conidia

value: CEA17 delta_akuB::KU88

value: {delta}rrpA/B

value: 0 h


title: 𝚫rrpA/B_conidia_3

description:
50-bp single read sequencing
rrpAB_conidia_R3

value: CEA17 delta_akuB::KU89

value: Aspergillus minimal media agar plates


title: Dd_24-44cell_rep3


title: 𝚫ppdA/B_conidia_3

description:
50-bp single read sequencing
ppdAB_conidia_R3

value: CEA17 delta_akuB::KU86

value: {delta}ppdA/B


title: Sample 12

value: HeLa cells

value: NEAT1/MALAT1 inhibition

value: dCas9-SunTag + sgR-lncRNAs + 500 nM Bio-PDC


title: Dd_24-44cell_rep1

value: whole organism


title: Sample 10

value: WT

value: dCas9-SunTag + sgR-Ctrl + 500 nM Bio-PDC


title: Mouse A, Tumour, Day 8 IP, EYFP-

value: Tumour

value: EYFP- T cells


title: TM4_MEHP_rep2

city: Beijing

first: LI

middle: Yong

last: Ning

address: 7 Panjiayuan Nanli

institute: China National Center for Food Safety Risk Assessment

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference  genome  and  gene  model  annotation  files  were  downloaded  from  genome  website directly.  Index  of the  reference  genome  was  built  using  Hisat2  v2.0.5  and  paired-end  clean reads  were  aligned  to  the  reference  genome  using  Hisat2  v2.0.5.  We  selected  Hisat2  as  the mapping  tool  for  that  Hisat2  can  generate  a  database  of splice junctions  based  on  the  gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The  mapped  reads  of each  sample  were  assembled  by  StringTie  (v1.3.3b)(Mihaela  Pertea.et al.  2015)  in  a  reference-based  approach.  StringTie  uses  a  novel  network  flow  algorithm  as well  as  an  optional  de  novo  assembly  step  to  assemble  and  quantitate  fulllength  transcripts representing multiple splice variants for each gene locus.
featureCounts  v1.5.0-p3  was  used  to  count  the  reads  numbers  mapped  to  each  gene.  And then  FPKM  of each  gene  was  calculated  based  on  the  length  of the  gene  and  reads  count mapped  to  this  gene.  FPKM,  expected  number  of  Fragments  Per  Kilobase  of  transcript sequence  per  Millions  base  pairs  sequenced,  considers  the  effect  of  sequencing  depth  and gene  length  for the reads  count  at the  same time,  and  is  currently the most  commonly used method  for  estimating  gene  expression  levels.
(For    DESeq2    with    biological    replicates)    Differential    expression    analysis    of    two conditions/groups  (two  biological  replicates  per  condition)  was  performed  using  the  DESeq2 R   package    (1.20.0).   DESeq2   provide    statistical   routines   for   determining   differential expression  in  digital  gene  expression  data  using  a  model  based  on  the  negative  binomial distribution.   The   resulting   P-values   were   adjusted   using   the   Benjamini   and   Hochberg's approach  for  controlling  the  false  discovery  rate  .  Genes  with  an  adjusted  P-value  <0.05 found by DESeq2 were assigned as differentially expressed. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one  scaling  normalized  factor.  Differential  expression  analysis  of  two  conditions  was performed  using  the  edgeR  R  package  (3 22 5)   The  P  values  were  adjusted  using  the Benjamini  & Hochberg method.  Corrected P-value  of 0.05  and  absolute  foldchange  of 2 were set as the threshold for significantly differential expression.
Gene Ontology(GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected  Pvalue  less  than  0.05  were  considered  significantly  enriched  by  differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological  system,  such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing        and         other        high-through         put        experimental       technologies  (http://www.genome.jp/kegg/).  We  used  clusterProfiler  R  package  to  test  the  statistical enrichment of differential expression genes in KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text film includes raw conuts for each Sample

source_name: Rat TM4

growth_protocol: TM3 and TM4 cells were cultured in DMEM/F-12 (1:1) medium (Gibco, 21041025) supplemented with 2.5% FBS (Gibco, 10270106), 5% fetal equine serum (Solarbio, S9050), 1% MEM NEAA (Gibco, 11140050), and 1% penicillin-streptomycin (Gibco, 15140122). The cell lines were maintained at 37 ℃ with 5% CO2

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified  from total  RNA using poly-T  oligo-attached magnetic beads.  Fragmentation was carried  out  using  divalent  cations  under  elevated  temperature  in  First  Strand  Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV   Reverse   Transcriptase(RNase   H-).    Second    strand   cDNA    synthesis   was subsequently performed using DNA Polymerase I and RNase H.Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3'ends of  DNA  fragments,  Adaptor  with  hairpin  loop  structure  were  ligated  to  prepare  for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system(Beckman Coulter, Beverly, USA). Then  PCR was performed with  Phusion  High-Fidelity  DNA polymerase,  Universal  PCR  primers and Index(X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The  clustering  of the  index-coded  samples  was performed  on  a  cBot  Cluster  Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: TM3 Leydig and TM4 Sertoli cells were exposed to 100 uM MEHP for 72 hours, 0.1% DMSO was used as a control.

value: Rat TM4

value: testicular Sertoli cell

tag: time

value: 72 hours

value: 100 uM MEHP


title: 𝚫ppdA/B_conidia_1

description:
50-bp single read sequencing
ppdAB_conidia_R1

value: conidia

value: CEA17 delta_akuB::KU84

value: 0 h


title: TM4_MEHP_rep3


title: TM4_MEHP_rep1


title: Dd_24-44cell_rep2


title: Mouse A, Spleen, Day 8 IP, EYFP-

value: Spleen

value: 8 days after intraperitoneal tamoxifen

value: Other


title: Mouse A, Tumour, Day 8 IP, EYFP+

value: EYFP+ T cells


title: Sample 9

value: HeLa cells


title: Dd_64-78cell_rep2

value: whole organism


title: Dd_64-78cell_rep3


title: 𝚫rrpA/B_conidia_1

description:
50-bp single read sequencing
rrpAB_conidia_R1

value: CEA17 delta_akuB::KU87

value: Aspergillus minimal media agar plates

value: {delta}rrpA/B


title: Sample 11

value: NEAT1/MALAT1 inhibition

value: dCas9-SunTag + sgR-lncRNAs + 500 nM Bio-PDC


title: 𝚫ppdA/B_conidia_2

description:
50-bp single read sequencing
ppdAB_conidia_R2

value: CEA17 delta_akuB::KU85

value: {delta}ppdA/B


title: 𝚫dclA/B_conidia_3

description:
50-bp single read sequencing
dclAB_conidia_R3

value: CEA17 delta_akuB::KU83

value: {delta}dclA/B


title: Dd_8-cell_rep5


title: TM4_DMSO_rep3

value: Rat TM4

value: testicular Sertoli cell

value: 72 hours

value: 0.1percent DMSO


title: Dd_8-cell_rep4


title: Sample 7

value: dCas9-SunTag + sgR-lncRNAs + 200 nM Bio-PDC


title: Dd_8-cell_rep2


title: 𝚫dclA/B_conidia_2

description:
50-bp single read sequencing
dclAB_conidia_R2

value: conidia

value: CEA17 delta_akuB::KU82

value: 0 h


title: 𝚫dclA/B_conidia_1

description:
50-bp single read sequencing
dclAB_conidia_R1

value: CEA17 delta_akuB::KU81


title: TM4_DMSO_rep2


title: Wild-type_conidia_2

description:
50-bp single read sequencing
CEA17_conidia_R2

value: CEA17 delta_akuB::KU80

value: Aspergillus minimal media agar plates

value: wild type


title: Dd_8-cell_rep3

value: whole organism


title: Sample 4

value: HeLa cells

value: NEAT1/MALAT1 inhibition

value: dCas9-SunTag + sgR-lncRNAs + 500 nM Bio-PDC


title: Dd_8-cell_rep1


title: TM3_MEHP_rep2

source_name: Rat TM3

value: Rat TM3

value: testicular Leydig cell

value: 100 uM MEHP


title: Sample 6

value: WT

value: dCas9-SunTag + sgR-Ctrl + 200 nM Bio-PDS


title: Dd_4-cell_rep5


title: TM3_MEHP_rep3

value: 72 hours


title: Sample 5


title: Wild-type_conidia_3

description:
50-bp single read sequencing
CEA17_conidia_R3

value: conidia


title: Sample 3


title: Wild-type_conidia_1

description:
50-bp single read sequencing
CEA17_conidia_R1


title: pol3pip H3K4me3_eSPAN 25C 30' MNase rep2 [Alb765_pol3pip_H3K4me3_eSPAN_S30]

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
Raw reads were firstly trimmed by Cutadapt (Marcel, 2011) to remove adapters and low quality reads, and then mapped to the yeast genome (sacCer3) using Bowtie2 (Langmead and Salzberg, 2012).Duplicate reads were further filtered by Sambamba (Tarasov et al., 2015) to remove PCR duplication.
The genome-wide read coverage on Watson and Crick strands were calculated at the bin of 1bp using deepTools bamCoverage (Ramirez et al., 2016). Then, the raw genome-wide read coverage was normalized with the number of total mapped reads to obtain counts per million value (CPM).
Spike-in added samples normalization. For each Sonication-BrdU-IP-ssSeq sample, the raw genome-wide coverage was normalized using the formula: BrdUsoni = (BrdUcov / BrdUspike) / (Inputread / Inputspike). BrdUcov is the raw coverage of BrdU-IP-ssSeq; BrdUspike is the number of total mapped spike-in reads (S. pombe reads) in BrdU sample, Inputread is the number of total mapped reads in input, and Inputspike is the number of total mapped spike-in reads (S. pombe) in input. In this way, BrdU incorporation at each strain was quantified as BrdUsoni.
Spike in added samples normalization. For each MNase-BrdU-IP-ssSeq dataset, reads with the nucleosome sized (120~170bp) were first selected to calculate the raw coverage of nucleosome occupancy surrounding replication origins, and then normalized using the formula: BrdUMNase = (BrdUcov-MNase / BrdUspike-MNase) / (Inputread-MNase / Inputspike-MNase). BrdUcov-MNase is the raw coverage of the nucleosome-sized reads, BrdUspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same sample, Inputread-MNase is the number of mapped  nucleosome-sized reads in input, and Inputspike-MNase is the number of mapped nucleosome-sized spike-in reads in the same input sample. In this way, the nucleosome occupancy on nascent chromatin was quantified as BrdUMNase.
Assembly: saccer3
Supplementary files format and content: tar of bw, bigwig format, CPM which is normalized by total number of reads
Supplementary files format and content: tar of bw, bigwig format, BrdU coverage normalized by spike-in and input described as formulas above.

organism: Saccharomyces cerevisiae

source_name: pol3pip H3K4me3_eSPAN 25C 30' MNase

growth_protocol: For most experiments, yeast cells were cultured and synchronized at G1 phase following standard procedures (Dunham et al., 2015). ChIP, BrdU-IP-ssSeq, and eSPAN sample collection was performed as described previously (Gan et al., 2017; Yu et al., 2018). Briefly, exponentially growing yeast cultures at OD600=0.4-0.5 were synchronized by adding a-factor at 5mg/ml and arrested for 3h at 25°C.

extract_protocol:
For analysis of DNA replication by BrdU-IP-ssSeq, and PCNA ChIP and eSPAN experiments, chromatin was fragmented by sonication (15 seconds on and 30 seconds off for 10 cycles in a Bioruptor Pico, Diagenode). For analysis of nucleosome occupancy at nascent chromatin, H3K4me3 and H3K56ac ChIP as well as almost all eSPAN experiments except those marked by sonication, chromatin was digested with MNase to map nucleosomes (Wal and Pugh, 2012).
The ssDNA libraries were prepared using the Accel-NGS 1S Plus kit (Cat no. 10096, Swift Bioscience).

treatment_protocol: Cells were then released into fresh YPD medium containing 400mg/ml BrdU without HU for 30 or 40 minutes at 25°C. For experiments using auxin-inducible protein degradation mutant strains, 1mM IAA or the equivalent volume of ethanol was added to the arresting culture (30 minutes before release) and cells were released in YPD medium also containing IAA or ethanol.

tag: batch

tag: strain

tag: condition

value: 25C 30' MNase


title: Dd_4-cell_rep4


title: TM3_MEHP_rep1


title: Mouse 1-5, Spleen, Day 8 IT, CSP

description: 10X Genomics

library_source: other

data_processing:
Raw FASTQ files of the gene expression library were analysed using 10x Genomics Cell Ranger software.
Generated count matrices were analyzed using Seurat and Scanpy (demultiplexing, quality control, normalization, clustering and differential gene expression)
Assembly: mm10
Supplementary files format and content: Comma-separated/ tab-separated values files, matrix and annotated data matrix files.

molecule: other

extract_protocol:
Freshly collected cells were sorted into PBS containing 10%FCS and 2mM EDTA in cold and spun down at 300g 7minutes 4°C before resuspension in PBS.
Single-cell RNA-seq libraries were prepared using Chromium Single Cell and V(D)J Enrichment Kits following the Single-Cell V(D)J Reagent Kits User Guide (Manual Part CG000086 Rev H, I, J, K, L, M; 10X Genomics). The data from the experiment using intraperitoneal tamoxifen were generated using chemistry (5’ v 1) before the introduction of dual-indexing strategy; the data for the intratumoural experiment was generated using chemistry (5’ v 2).

value: Spleen

value: EYFP+ T cells

value: 8 days after intratumoral tamoxifen

value: scRNA-seq HTO


title: Sample 2

value: dCas9-SunTag + sgR-Ctrl + 500 nM Bio-PDC


title: Sample 8

value: dCas9-SunTag + sgR-lncRNAs + 200 nM Bio-PDC


title: Sample 1

value: HeLa cells


title: Dd_4-cell_rep3

value: whole organism


title: Dd_4-cell_rep1


title: Dd_4-cell_rep2


title: 19476X8 RFP-GBM11-chim 2

city: Salt Lake City

first: Simone

last: Chiola

department: Neurobiology

institute: University of Utah

library_source: transcriptomic single cell

data_processing:
The Fastq files were aligned to the refdata-gex-GRCh38-2020-A human reference from 10X genomics using cellranger count version 6.0.1.
Assembly: hg38
Supplementary files format and content: Filtered gene barcode matrices in H5 format

source_name: Chimeras

extract_protocol:
SNR-derived organoids and chimeras were rinsed with sterile Dulbecco’s phosphate-buffered saline (DPBS, 1X) and chopped in small pieces using a scalpel. Organoids’ pieces were collected in 1.5 mL tubes in DPBS and centrifuged 573 for 2 minutes at 1000 rpm. Samples were incubated in pre-warmed papain (Worthington Biochemical) containing 5% DNaseI (Sigma) at 37oC for 50 minutes. After incubation, cells were resuspended in Trypsin Inhibitor (Sigma) and manually triturated by pipetting up and down using P1000 pipette. Cells were centrifuged for 5 minutes at 1000 rpm before the next step. Cells were resuspended in cold DPBS containing 0.04% BSA. Samples were kept on ice from this point forward. Samples were quickly transferred to the High Throughput Genomics Core Facility at the University of Utah for cell viability assessment.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Chimeras

value: neural and tumor cells

value: IWR


title: TM3_DMSO_rep3

value: Rat TM3

value: testicular Leydig cell

value: 0.1percent DMSO


title: TM3_DMSO_rep1

value: 72 hours


title: MDA-MB-231 cells, Vector control, Olaparib treatment

first: Hanqiu

last: Zheng

address: Haidian District

institute: Tsinghua university

data_processing:
The quality of Illumina RNA sequences were controlled by using FastQC
Illumina adapter sequences have been trimmed off
the remaining sequences were subsequently mapped against the GRCh38 human reference using STAR
The output SAM files were converted into sort BAM files by Samtools
The counts for each gene were obtained by using featureCounts
Assembly: GRCh38 human
Supplementary files format and content: CSV files include CPM normalized counts for each Sample

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was collected using Trizol (Takara, Cat # 9108) according to the manufacturer’s instruction.
Libraries were constructed using NEBNext Ultra II Directional RNA library Prep Kit for Illumina according to the manufacturer’s instruction (NEB, Cat # E7765S).

treatment_protocol: Cells were then treated with either 40 μM DMSO or Olaparib for 3 days.

value: human breast cancer cell line

value: WT

value: 40 μM Olaparib for 3 days


title: TM3_DMSO_rep2


title: MDA-MB-231 cells, ARL11 overexpression, Olaparib treatment

value: ARL11 overexpression


title: 19476X7 GBM11

source_name: Spheroids

value: Spheroids

value: tumor cells


title: Mouse 4, Tumour, Day 8 IT, CSP

description: 10X Genomics

source_name: Tumour

value: Tumour

value: EYFP+ T cells

value: 8 days after intratumoral tamoxifen

value: scRNA-seq HTO


title: Mouse 3 and 5, Tumour, Day 8 IT, VDJ

description: 10X Genomics

molecule: polyA RNA

value: scRNA-seq TCR


title: Mouse 3 and 5, Tumour, Day 8 IT, CSP

description: 10X Genomics


title: TM4_DMSO_rep1

value: Rat TM4

value: testicular Sertoli cell


title: Mouse 1-5, Spleen, Day 8 IT, VDJ

description: 10X Genomics

value: Spleen


title: Dd_2-cell_rep5

source_name: whole organism

value: whole organism


title: 19476X5 RFP-GBM11-chim 1 plus H9-GBM11-chim 1

value: Chimeras

value: neural and tumor cells


title: Dd_2-cell_rep4


title: Dd_2-cell_rep3


title: Mouse 4, Tumour, Day 8 IT, VDJ

description: 10X Genomics


title: MDA-MB-231 cells, Vector control, DMSO treatment

value: human breast cancer cell line

value: 40 μM DMSO for 3 days


title: Dd_2-cell_rep2


title: 19476X4 RFP-GBM20-chim 3 plus H9-GBM20-chim 1


title: Mouse 1 and 2, Tumour, Day 8 IT, VDJ

description: 10X Genomics


title: Mouse 1 and 2, Tumour, Day 8 IT, CSP

description: 10X Genomics


title: Dd_2-cell_rep1


title: 19476X3 RFP-iPSCs-orgs 3 plus H9-ESCs-orgs 1

source_name: Telencephalic organoids

value: Telencephalic organoids

value: neural cells


title: 19476X6 GBM20

value: Spheroids


title: Mouse 1-5, Spleen, Day 8 IT, GEX

description: 10X Genomics

source_name: Spleen

value: scRNA-seq GEX


title: MDA-MB-231 cells, ARL11 overexpression, DMSO treatment

value: ARL11 overexpression


title: Dd_Zygote_rep4


title: LoVo cells, Tet-On shRNA, Day 5

city: NOVATO

first: Yaofu

state: California

address: 1599 S NOVATO BLVD

institute: Buck Institute for Research on Ag

data_processing:
Clc Genomics Workbench
Assembly: mm10
Supplementary files format and content: EXCEL
Supplementary files format and content: EXCEL

source_name: Colon

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS; Gibco, 10099141), 2 mM of L-glutamine, 100 U of penicillin and 100 mg/ml of streptomycin, and incubated at 37°C with 5% CO 2 .

extract_protocol:
Total RNAs from HRD1-KD cells exposed to Dox for the indicated times was extracted using RNAiso Plus Reagent.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit folowing manufacturer's protocols.

treatment_protocol: Cells were treated with doxycycline (Dox, 1 μg/ml) to induce HRD1 knockdown

value: Colon

value: LoVo cells

value: epithelial cell

value: HRD1 inducable knockdown

value: Dox Induce 5 day


title: Mouse 3 and 5, Tumour, Day 8 IT, GEX

description: 10X Genomics

value: Tumour

value: EYFP+ T cells

value: 8 days after intratumoral tamoxifen


title: 19476X2 RFP-GBM20-chim 2

value: Chimeras

value: IWR


title: 19040X2 RFP-GBM20-chim 1

value: neural and tumor cells


title: Mouse 4, Tumour, Day 8 IT, GEX

description: 10X Genomics


title: Mouse 1 and 2, Tumour, Day 8 IT, GEX

description: 10X Genomics


title: 19476X1 RFP-iPSCs-orgs 2

value: RFP-iPSCs


title: Dd_Zygote_rep1

value: whole organism


title: 19040X1 RFP-iPSCs-orgs 1

value: Telencephalic organoids

value: neural cells


title: LoVo cells, Tet-On shRNA, Day 3

value: Dox Induce 3 day


title: Dd_Zygote_rep2


title: Esophagus, (Strain), Sample1

city: Pohang

first: Somi

last: Kim

address: 47, Jigok-ro

department: Life Sciences

country: South Korea

institute: POSTECH

description: Wild-type cells were sorted in wells [(C,D,G,H)1-24]; Sox2-mutant cells were sorted in [(A,B,E,F)1-24,I10-24]

data_processing:
Raw FASTQ files for scRNA-seq were processed by using the zUMIs (v2.9.7) pipeline and reads were aligned to the mouse reference genome (mm10) using the STAR aligner (v2.7.3) with the whitelist of cell barcodes and the fasta file of ERCC spike-in sequences were used.
Assembly: mm10
Supplementary files format and content: FASTQ and R Data Serialization files

source_name: Esophagus

extract_protocol:
Esophageal cells were isolated from 4-week induced Rosa-CreERT2; Red2Flpe; Sox2scon/scon mice and single cell sorted into 384-well plates.
Cells were heat-lysed at 65° C followed by cDNA synthesis was done using the CEL-Seq2 protocol with a robotic liquid handling platforms Nanodrop II (GC Biotech) and Mosquito (TTP Labtech).

treatment_protocol: Tamoxifen-induced Cre recombination to generate wild-type and Sox2-mutant cells

value: Esophagus

value: primary cells

value: Epithelial

value: Tamoxifen


title: Esophagus, (Strain), Sample2

description: Wild-type cells were sorted in wells [(C,D,G,H,K,L)1-24, O1-22, P1-22; Sox2-mutant cells were sorted in wells [(A,B,E,F,I,J,M,N)1-24]


title: BMDMs, shWTAP, rep3

status: Public on May 24 2024

first: Yuman

last: Li

address: No.22 , Zhongguancun South Avenue, Haidian District, Beijing

institute: Peking University School and Hospital of Stomatology

description: shWTAP3 TPM

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.6).
Bowtie2 (2.3.4.3) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: Mus_musculus.GRCm38 V101
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: bone marrow

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard BGISEQ protocols.

value: bone marrow

value: bone marrow-derived macrophages

value: WTAP knockdown


title: LoVo cells, Tet-On shRNA, Day 0

value: Colon

value: LoVo cells

value: epithelial cell

value: HRD1 inducable knockdown

value: Dox Induce 0 day


title: BMDMs, shWTAP, rep2

description: shWTAP2 TPM


title: BMDMs, shWTAP, rep1

description: shWTAP1 TPM


title: BMDMs, shNC, rep2

description: shNC2 TPM

value: WT


title: BMDMs, shNC, rep 1

description: shNC1 TPM


title: BMDMs, shNC, rep3

description: shNC3 TPM


title: DO560_ORSAM20500_GT21-11115_M_heart

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Assembly: GRCm38
Each tissue directory has a raw counts matrix, a vst matrix and mrna annotations table.  counts_matrix.csv: raw counts quantified by EMASE and processed by/RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script.  vst_matrix.csv: counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation). Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/QTLviewer_format.R script.  mrna_annots.csv: gene annotation file ENSEMBL version 75.
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv

source_name: heart

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step.
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction. Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification. The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

treatment_protocol: Diversity Outbred mice were sensitized on a high-fat, high-sugar (HFHS) diet

value: heart

tag: diet

value: 45% fat


title: DO559_ORSAM20499_GT21-11004_M_heart


title: DO558_ORSAM20498_GT21-10999_M_heart


title: DO557_ORSAM20497_GT21-11054_M_heart


title: DO555_ORSAM20495_GT21-11073_M_heart


title: Dd_Zygote_rep3

data_processing:
sequence read was trimmed for adaptor sequence/low-quality using fastp (v0.20.1) software
read count extraction and normalization were performed using RSEM29 (v1.2.28)
Assembly: The genome used in this study was sequenced and assembled in our own laboratory and has not yet been published.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
RNA was harvested by treating eggs with lysis buffer. Details can refer to smart-seq2 peotocols.
RNA libraries for RNA-seq were prepared using Smart-seq2 protocols.

value: whole organism


title: DO554_ORSAM20494_GT21-10964_M_heart


title: DO556_ORSAM20496_GT21-11042_M_heart


title: DO553_ORSAM20493_GT21-11003_M_heart


title: DO552_ORSAM20492_GT21-11103_M_heart


title: DO550_ORSAM20490_GT21-10933_M_heart


title: DO551_ORSAM20491_GT21-10919_M_heart


title: DO548_ORSAM20488_GT21-10923_M_heart


title: DO547_ORSAM20487_GT21-11114_M_heart


title: DO544_ORSAM20484_GT21-11116_M_heart


title: DO543_ORSAM20483_GT21-11011_M_heart


title: DO539_ORSAM20479_GT21-10916_M_heart


title: DO546_ORSAM20486_GT21-10971_M_heart


title: DO540_ORSAM20480_GT21-10917_M_heart


title: DO542_ORSAM20482_GT21-11043_M_heart


title: DO537_ORSAM20477_GT21-10926_M_heart


title: DO538_ORSAM20478_GT21-11069_M_heart


title: DO541_ORSAM20481_GT21-11049_M_heart


title: DO535_ORSAM20475_GT21-10992_M_heart


title: DO536_ORSAM20476_GT21-11038_M_heart


title: DO534_ORSAM20474_GT21-10980_M_heart


title: DO532_ORSAM20472_GT21-10946_M_heart


title: DO530_ORSAM20470_GT21-10976_M_heart


title: DO531_ORSAM20471_GT21-11009_M_heart


title: DO529_ORSAM20469_GT21-11088_M_heart


title: DO528_ORSAM20468_GT21-10996_M_heart


title: DO533_ORSAM20473_GT21-10939_M_heart


title: DO549_ORSAM20489_GT21-11060_M_heart


title: DO524_ORSAM20464_GT21-10945_M_heart


title: DO545_ORSAM20485_GT21-11047_M_heart


title: DO526_ORSAM20466_GT21-10989_M_heart


title: DO527_ORSAM20467_GT21-11045_M_heart


title: DO522_ORSAM20462_GT21-11033_M_heart


title: DO520_ORSAM20460_GT21-10936_M_heart


title: DO521_ORSAM20461_GT21-10930_M_heart


title: DO523_ORSAM20463_GT21-11095_M_heart


title: DO519_ORSAM20459_GT21-10990_M_heart


title: DO513_ORSAM20453_GT21-11048_M_heart


title: DO514_ORSAM20454_GT21-10929_M_heart


title: DO515_ORSAM20455_GT21-10940_M_heart


title: DO525_ORSAM20465_GT21-10956_M_heart


title: DO510_ORSAM20450_GT21-11089_F_heart


title: DO511_ORSAM20451_GT21-11080_M_heart


title: DO505_ORSAM20446_GT21-10951_F_heart


title: DO508_ORSAM20449_GT21-10947_F_heart


title: DO507_ORSAM20448_GT21-11111_F_heart


title: DO504_ORSAM20445_GT21-10920_F_heart


title: DO502_ORSAM20443_GT21-11022_F_heart


title: DO501_ORSAM20442_GT21-11031_F_heart


title: DO500_ORSAM20441_GT21-11057_F_heart


title: DO499_ORSAM20440_GT21-10937_F_heart


title: DO498_ORSAM20439_GT21-10974_F_heart


title: DO497_ORSAM20438_GT21-10981_F_heart


title: DO496_ORSAM20437_GT21-10961_F_heart


title: DO495_ORSAM20436_GT21-11016_F_heart


title: DO494_ORSAM20435_GT21-11098_F_heart


title: DO518_ORSAM20458_GT21-11029_M_heart


title: DO512_ORSAM20452_GT21-11046_M_heart


title: DO517_ORSAM20457_GT21-11021_M_heart


title: DO490_ORSAM20431_GT21-11067_F_heart


title: DO493_ORSAM20434_GT21-11081_F_heart


title: DO516_ORSAM20456_GT21-10960_M_heart


title: DO489_ORSAM20430_GT21-10918_F_heart


title: DO491_ORSAM20432_GT21-11063_F_heart


title: DO488_ORSAM20429_GT21-10970_F_heart


title: DO486_ORSAM20427_GT21-11018_F_heart


title: DO506_ORSAM20447_GT21-10966_F_heart


title: DO485_ORSAM20426_GT21-11050_F_heart


title: DO487_ORSAM20428_GT21-11007_F_heart


title: DO484_ORSAM20425_GT21-10969_F_heart


title: DO482_ORSAM20423_GT21-11110_F_heart


title: DO503_ORSAM20444_GT21-11034_F_heart


title: DO481_ORSAM20422_GT21-10948_F_heart


title: DO480_ORSAM20421_GT21-11062_F_heart


title: DO483_ORSAM20424_GT21-11001_F_heart


title: DO478_ORSAM20419_GT21-11101_F_heart


title: DO476_ORSAM20417_GT21-10927_F_heart


title: DO473_ORSAM20414_GT21-11019_F_heart


title: DO492_ORSAM20433_GT21-10958_F_heart


title: DO472_ORSAM20413_GT21-10952_F_heart


title: DO474_ORSAM20415_GT21-10975_F_heart


title: DO471_ORSAM20412_GT21-10941_F_heart


title: DO477_ORSAM20418_GT21-10979_F_heart


title: DO470_ORSAM20411_GT21-11012_F_heart


title: DO467_ORSAM20408_GT21-11041_F_heart


title: DO463_ORSAM20404_GT21-11076_F_heart


title: DO475_ORSAM20416_GT21-11093_F_heart


title: DO466_ORSAM20407_GT21-10931_F_heart


title: DO464_ORSAM20405_GT21-10921_F_heart


title: DO469_ORSAM20410_GT21-10965_F_heart


title: DO462_ORSAM20403_GT21-11028_F_heart


title: DO420_ORSAM20402_GT21-10954_M_heart


title: DO416_ORSAM20400_GT21-11107_M_heart


title: DO468_ORSAM20409_GT21-11000_F_heart


title: DO417_ORSAM20401_GT21-11079_M_heart


title: DO414_ORSAM20398_GT21-11061_M_heart


title: DO479_ORSAM20420_GT21-11027_F_heart


title: DO415_ORSAM20399_GT21-11097_M_heart


title: DO413_ORSAM20397_GT21-11083_M_heart


title: DO412_ORSAM20396_GT21-11024_M_heart


title: DO411_ORSAM20395_GT21-11005_M_heart


title: DO408_ORSAM20392_GT21-11074_M_heart


title: DO409_ORSAM20393_GT21-11002_M_heart


title: DO407_ORSAM20391_GT21-11085_M_heart


title: DO406_ORSAM20390_GT21-10928_M_heart


title: DO405_ORSAM20389_GT21-11087_M_heart


title: DO404_ORSAM20388_GT21-11056_M_heart


title: DO465_ORSAM20406_GT21-10998_F_heart


title: DO403_ORSAM20387_GT21-11025_M_heart


title: DO401_ORSAM20385_GT21-11100_M_heart


title: DO400_ORSAM20384_GT21-10942_M_heart


title: DO402_ORSAM20386_GT21-11109_M_heart


title: DO399_ORSAM20383_GT21-11055_M_heart


title: DO398_ORSAM20382_GT21-10944_M_heart


title: DO392_ORSAM20376_GT21-10994_M_heart


title: DO397_ORSAM20381_GT21-11037_M_heart


title: DO387_ORSAM20371_GT21-11032_M_heart


title: DO389_ORSAM20373_GT21-11075_M_heart


title: DO395_ORSAM20379_GT21-11096_M_heart


title: DO390_ORSAM20374_GT21-10982_M_heart


title: DO410_ORSAM20394_GT21-11052_M_heart


title: DO396_ORSAM20380_GT21-11058_M_heart


title: DO386_ORSAM20370_GT21-10987_M_heart


title: DO393_ORSAM20377_GT21-10984_M_heart


title: DO394_ORSAM20378_GT21-11105_M_heart


title: DO391_ORSAM20375_GT21-11008_M_heart


title: DO388_ORSAM20372_GT21-11099_M_heart


title: DO382_ORSAM20366_GT21-11108_M_heart


title: DO381_ORSAM20365_GT21-10935_M_heart


title: DO385_ORSAM20369_GT21-10977_M_heart


title: DO383_ORSAM20367_GT21-10997_M_heart


title: DO379_ORSAM20363_GT21-11104_M_heart


title: DO377_ORSAM20361_GT21-11014_M_heart


title: DO376_ORSAM20360_GT21-11036_M_heart


title: DO375_ORSAM20359_GT21-11026_M_heart


title: DO374_ORSAM20358_GT21-10967_M_heart


title: DO372_ORSAM20356_GT21-11106_M_heart


title: DO373_ORSAM20357_GT21-10983_M_heart


title: DO371_ORSAM20355_GT21-11051_M_heart


title: DO370_ORSAM20354_GT21-10943_F_heart


title: DO369_ORSAM20353_GT21-10922_F_heart


title: DO384_ORSAM20368_GT21-10972_M_heart


title: DO368_ORSAM20352_GT21-11010_F_heart


title: DO365_ORSAM20349_GT21-10938_F_heart


title: DO361_ORSAM20345_GT21-10985_F_heart


title: DO363_ORSAM20347_GT21-10932_F_heart


title: DO380_ORSAM20364_GT21-10991_M_heart


title: DO360_ORSAM20344_GT21-11102_F_heart


title: DO362_ORSAM20346_GT21-11065_F_heart


title: DO358_ORSAM20342_GT21-11092_F_heart


title: DO364_ORSAM20348_GT21-11023_F_heart


title: DO355_ORSAM20339_GT21-10968_F_heart


title: DO354_ORSAM20338_GT21-10949_F_heart


title: DO353_ORSAM20337_GT21-11053_F_heart


title: DO359_ORSAM20343_GT21-11015_F_heart


title: DO378_ORSAM20362_GT21-11090_M_heart


title: DO350_ORSAM20335_GT21-11020_F_heart


title: DO352_ORSAM20336_GT21-10955_F_heart


title: DO356_ORSAM20340_GT21-11094_F_heart


title: DO349_ORSAM20334_GT21-10925_F_heart


title: DO348_ORSAM20333_GT21-10978_F_heart


title: DO347_ORSAM20332_GT21-10934_F_heart


title: DO346_ORSAM20331_GT21-11071_F_heart


title: DO345_ORSAM20330_GT21-11030_F_heart


title: DO344_ORSAM20329_GT21-11035_F_heart


title: DO343_ORSAM20328_GT21-10950_F_heart


title: DO367_ORSAM20351_GT21-10924_F_heart


title: DO342_ORSAM20327_GT21-10995_F_heart


title: DO366_ORSAM20350_GT21-11070_F_heart


title: DO340_ORSAM20326_GT21-11066_F_heart


title: DO339_ORSAM20325_GT21-11117_F_heart


title: DO337_ORSAM20323_GT21-10988_F_heart


title: DO333_ORSAM20320_GT21-11112_F_heart


title: DO357_ORSAM20341_GT21-11113_F_heart


title: DO338_ORSAM20324_GT21-10962_F_heart


title: DO332_ORSAM20319_GT21-10959_F_heart


title: DO335_ORSAM20321_GT21-11078_F_heart


title: DO327_ORSAM20314_GT21-11040_F_heart


title: DO325_ORSAM20312_GT21-10973_F_heart


title: DO328_ORSAM20315_GT21-11017_F_heart


title: DO326_ORSAM20313_GT21-11044_F_heart


title: DO330_ORSAM20317_GT21-11082_F_heart


title: DO331_ORSAM20318_GT21-11084_F_heart


title: DO324_ORSAM20311_GT21-11086_F_heart


title: DO329_ORSAM20316_GT21-11077_F_heart


title: DO323_ORSAM20310_GT21-10953_F_heart


title: DO322_ORSAM20309_GT21-10963_F_heart


title: Splenic NK cells GEX

city: Bethesda

first: Avinash

last: Bhandoola

state: MD

address: 10 Center Dr

institute: NCI

description:
GEX: Fastq files contain data as according to standard 10X genomcis pipeline
Spleen_NK_filtered_feature_bc_matrix.h5

data_processing:
Base calling was performed using RTA 3.9.25, demultiplexing was performed using cellranger v6.1.1 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v6.1.1 (STAR 2.7.2a).
Assembly: mm10
Supplementary files format and content: h5 files
Library strategy: CITE-Seq

extract_protocol:
cells were isolated from bone marrow or spleen
scRNA-seq libraries were prepared using 10X Genomics Single Cell 3’ Reagent Kits v3.1, according to the manufacturer’s instructions

value: Spleen

value: NK cells

tag: age

value: 6-18 weeks

value: Adoptive transfer

value: mRNA


title: Splenic NK cells ADT

description:
HTO: Fastq files contain data as according to standard 10X genomcis pipeline
Spleen_NK_filtered_feature_bc_matrix.h5

molecule: protein

value: HTO


title: NK cells and ILC1s

description: BAM files contain mapped data

data_processing:
Base calling was performed using RTA 3.9.25, demultiplexing was performed using cellranger v6.1.1 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v6.1.1 (STAR 2.7.2a).
Assembly: mm10
Supplementary files format and content: h5 files

source_name: Bone marrow

value: Bone marrow

value: NK cells and ILC1s


title: CD122+ progenitors

description: BAM files contain mapped data

value: CD122+ progenitors


title: ILC progenitors (ALP, EILP, ILCP, ILC2P)

description: BAM files contain mapped data


title: DO321_ORSAM20308_GT21-11091_F_heart


title: Treatment3

city: Abu Dhabi

first: Muhammad

last: Arshad

state: Abu Dhabi

address: Saadiyat

country: United Arab Emirates

institute: New York University

data_processing:
Raw FASTQ sequenced reads were first assessed for quality using FastQC v0.11.5
The reads were then subjected to Trimmomatic v0.36 for quality trimming and adapter sequence removal.
After the quality trimming, the reads were assessed again with FastQC v0.11.5
The reads were aligned to the human reference genome GRCh38.p4 using HISAT2 with the default parameters and an additional –dta flag. The SAM alignments were then converted to BAM format and sorted coordinate using SAMtools v1.3.1.
The sorted BAM files were then passed through HTSeq-count v0.6.1p1 using the following options (-s no -t exon -I gene_id) for raw count generation. Concurrently, the sorted alignments were processed with Stringtie v1.3.0 for transcriptome quantification.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Brain

growth_protocol: U87MG cells were ordered from ATCC (HTB-14) and U87MG cells were cultured in DMEM, and then cells were supplemented with 10% heat-inactivated FBS, 50 IU/mL penicillin, and 50 μg/mL streptomycin in an incubator containing a humidified atmosphere of 95% air and 5% CO2 at 37 °C.

extract_protocol:
For the QC of purified RNA, absorbance ratios were assessed with NanoDrop 2000 spectrophotometer
Total RNA quality was evaluated based on the RNA integrity number (RIN) using a BioAnalyzer 2100 and quantified with a Qubit 4 Fluorometer. Next, RNA-Seq libraries were prepared using the NEB Next Ultra II RNA Library Prep Kit
Quantifying the pooled libraries required for RNA-seq was determined by real-time qPCR using a KAPA’s library quantification kit for the Illumina sequencing platforms. Pooled libraries were sequenced using the Illumina NextSeq 500/550 System with a Paired-end Mid Output v2 kit, 150 cycles.

treatment_protocol: The total RNA was extracted from U87MG (1 × 106cells in a 3 mL plate) treated with vehicle (control, n = 3), RSL3 (2 μM, n = 3) using the RNeasy Mini kit.

value: Brain

value: Human gliobalstoma

value: RSL3 (2 uM)


title: DO336_ORSAM20322_GT21-11072_F_heart


title: Treatment2


title: DO320_ORSAM20307_GT21-11064_M_heart


title: DO319_ORSAM20306_GT21-11068_M_heart


title: Treatment1


title: Control3

value: vehicle


title: DO318_ORSAM20305_GT21-11039_M_heart


title: Control2

value: WT


title: DO317_ORSAM20304_GT21-10957_M_heart

value: heart


title: Control1


title: DO315_ORSAM20302_GT21-11013_M_heart

value: 45% fat


title: DO316_ORSAM20303_GT21-11006_M_heart


title: siKLF-4

city: New Haven

first: Hanqiang

last: Deng

address: 116 Court Street

department: Yale Cardiovascular Research Center

institute: Yale University

data_processing:
Samples were subjected to RNA-sequencing using Illumina NextSeq 500 sequencer (75bp paired end reads).
The base calling data from sequencing were transferred into FASTQ files using bcl2fastq2 conversion software (version 2.20, Illumina).
The raw reads were aligned to the human reference genome GRCh38 using HISAT2 (version 2.1.0) alignment software and processed using HTSeq (version 0.11.1) to generate read counts for every gene.
DESeq2 (version 1.24, using default parameter) was used to pre-process raw data to remove the noise, normalize each sample to correct the batch effect, perform principal component analysis (PCA) for observing the similarity of replicates, and identify differential expression genes.
Assembly: human reference genome GRCh38
Supplementary files format and content: Excel includes raw counts for each sample
Supplementary files format and content: Excel includes log2(fold change) and FDR values for each sample

source_name: HUVEC

growth_protocol: HUVECs were maintained in EGM2 Endothelial Cells Growth Media (Lonza) and used for experiments between passage 2 and passage 5.

extract_protocol:
Total RNA was extracted from cells with RNeasy Plus Mini Kit (QIAGEN) according to the Manufacturer’s instructions.
RNA isolation and quality assessment, mRNA enrichment, cDNA synthesis, end repair, PCR amplification and library quantification.

treatment_protocol: Cells were transfected with Ctrl (siCtrl) or KLF2 (siKLF2) siRNA for 4 days.

value: HUVEC

value: primary endothelial cell

value: KLF2 knockdown

value: Day 4


title: siKLF-3


title: DO313_ORSAM20300_GT21-11059_M_heart


title: siKLF-2


title: siCTL-4


title: DO312_ORSAM20299_GT21-10986_M_heart


title: siKLF-1


title: DO311_ORSAM19559_GT21-08400_M_heart


title: DO310_ORSAM19558_GT21-08598_M_heart


title: siCTL-3


title: DO309_ORSAM19557_GT21-08373_M_heart


title: siCTL-1


title: DO308_ORSAM19556_GT21-08432_M_heart


title: siCTL-2


title: DO305_ORSAM19553_GT21-08644_M_heart


title: DO306_ORSAM19554_GT21-08418_M_heart


title: DO304_ORSAM19552_GT21-08508_M_heart


title: WT_ovaries_1_8st_M1BP_ChIP

city: Moscow

first: Marina

middle: Yu.

last: Mazina

address: Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
For ChIP-Seq data the single‐end reads in FastQ format were mapped to the Drosophila genome assembly dm6 using Bowtie2 (Galaxy Version 2.3.4.3) and filtered (with minimum MAPQ quality score = 5). BigWig files were generated using bamCoverage (Galaxy Version 3.5.1.0.0) with scores representing number of reads per kilobase per million (RPKM). The final BigWig files (representing the protein-binding profiles) were obtained using bigwigcompare (Galaxy Version 3.5.1.0.0) as a ratio of ChIP signal to Input.
Assembly: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary files format and content: bigwig

organism: Drosophila melanogaster

source_name: Ovaries were dissected from females 15 hours after eclosion

extract_protocol:
For the ChIP-Seq experiments ovaries were collected in PBS buffer (50 pairs per ChIP), cross-linked with 1% of formaldehyde for 5 min and then incubated for 5 min with 125 mM Glycine. After that ovaries were washed with PBS buffer for three times. The remaining ChIP protocol was performed as described previously (Vorobyeva et al (2013) NAR, 41:11, 5717–5730).
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

value: Oregon-R modENCODE (Bloomington stock 25211)

value: no treatment


title: WT_ovaries_1_8st_BEAF32_ChIP

source_name: Ovaries were dissected from females 15 hours after eclosion (containing egg chambers corresponding to 1-8 stages)


title: DO303_ORSAM19551_GT21-08612_M_heart


title: DO302_ORSAM19550_GT21-08575_M_heart


title: dsRedneg_NP15.6RNAi_10d_rep3

city: Philadelphia

first: Nancy

middle: M

last: Bonini

state: PA

address: 433 S University Ave

department: Biology

institute: University of Pennsylvania

data_processing:
Demultiplexed reads passing QC filter (Q > 30) were obtained from BaseSpace then merged across sequencing lanes for each sample, with approximately 20 million reads total per sample
Paired-end reads were aligned to the fly genome using HISAT2 (v2.1.0)
The HISAT2 index was built from FlyBase’s Drosophila melanogaster reference genome r6.17
Alignment sorted BAM files (samtools v.15) for each sample were merged across sequencing runs (picard)
Reads that uniquely aligned to exonic regions were counted with HTSeq (v0.9.1) with the union setting to produce a count matrix for differential expression analysis
Assembly: FlyBase’s Drosophila melanogaster reference genome r6.17
Supplementary files format and content: tab-separated text file includes raw counts for each sample

source_name: FACS sorted cells from whole brains

extract_protocol:
Total RNA was extract by trizol/chloroform and Zymo RNA clean and concentrator kit-5 (R1015)
RNA libraries for FACS sorted cells were prepred by Admera, using SMART-Seq V4 and NexteraXT Library Preparation. RNA lirbaries for whole brains were prepared by Admera, using TruSeq Stranded with Poly-A Selection

treatment_protocol: Treatment refers to feeding flies the geneSwitch activating drug RU-486

value: FACS sorted cells from whole brains

tag: cell type_(facs)

value: dsRedneg

value: RU-486 continuous, 29C

tag: biological replicate


title: dsRedneg_NP15.6RNAi_10d_rep2


title: dsRed+_NP15.6RNAi_10d_rep4

value: dsRed+


title: dsRedneg_NP15.6RNAi_10d_rep4


title: DO301_ORSAM19549_GT21-08427_M_heart


title: DO314_ORSAM20301_GT21-10993_M_heart


title: dsRedneg_NP15.6RNAi_10d_rep1


title: DO307_ORSAM19555_GT21-08461_M_heart


title: DO300_ORSAM19548_GT21-08452_M_heart


title: dsRed+_NP15.6RNAi_10d_rep2


title: dsRedneg_ND42RNAi_10d_rep4


title: DO299_ORSAM19547_GT21-08430_M_heart


title: dsRed+_NP15.6RNAi_10d_rep1


title: DO297_ORSAM19545_GT21-08485_M_heart


title: dsRedneg_ND42RNAi_10d_rep3


title: dsRedneg_ND42RNAi_10d_rep2


title: DO296_ORSAM19544_GT21-08627_M_heart


title: dsRed+_ND42RNAi_10d_rep4


title: DO293_ORSAM19541_GT21-08428_M_heart


title: dsRed+_ND42RNAi_10d_rep3


title: DO291_ORSAM19539_GT21-08375_M_heart


title: dsRed+_ND42RNAi_10d_rep1


title: dsRed+_ND42RNAi_10d_rep2


title: dsRed+_NP15.6RNAi_10d_rep3


title: DO292_ORSAM19540_GT21-08487_M_heart


title: DO290_ORSAM19538_GT21-08443_M_heart


title: DO298_ORSAM19546_GT21-08389_M_heart


title: AP1_blocked_ctrl_7d_rep3

data_processing:
Demultiplexed reads passing QC filter (Q > 30) were obtained from BaseSpace then merged across sequencing lanes for each sample, with approximately 20 million reads total per sample
Paired-end reads were aligned to the fly genome using HISAT2 (v2.1.0)
The HISAT2 index was built from FlyBase’s Drosophila melanogaster reference genome r6.17
Alignment sorted BAM files (samtools v.15) for each sample were merged across sequencing runs (picard)
Reads that uniquely aligned to exonic regions were counted with HTSeq (v0.9.1) with the union setting to produce a count matrix for differential expression analysis
Assembly: FlyBase’s Drosophila melanogaster reference genome r6.17
Supplementary files format and content: tab-seperated text file includes raw counts for each sample

source_name: whole brains

value: whole brains

value: repoGS>UAS-GFP


title: DO288_ORSAM19536_GT21-08424_M_heart


title: AP1_blocked_ctrl_7d_rep2


title: AP1_blocked_dFosDN_7d_rep3

value: repoGS>UAS-puckered


title: DO289_ORSAM19537_GT21-08536_M_heart


title: AP1_blocked_dFosDN_7d_rep2


title: AP1_blocked_puc_7d_rep3

value: repoGS>UAS-dFosDN


title: AP1_blocked_puc_7d_rep2


title: DO286_ORSAM19534_GT21-08385_M_heart


title: DO284_ORSAM19532_GT21-08580_M_heart


title: AP1_blocked_ctrl_7d_rep1


title: dsRedneg_ND42RNAi_10d_rep1


title: DO283_ORSAM19531_GT21-08617_M_heart


title: AP1_blocked_dFosDN_7d_rep1


title: DO295_ORSAM19543_GT21-08469_M_heart


title: DO294_ORSAM19542_GT21-08460_M_heart


title: DO282_ORSAM19530_GT21-08640_M_heart


title: AP1_blocked_ctrl_42d_rep3


title: DO280_ORSAM19528_GT21-08417_M_heart


title: DO281_ORSAM19529_GT21-08586_M_heart


title: AP1_blocked_puc_7d_rep1


title: AP1_blocked_puc_42d_rep3


title: DO279_ORSAM19527_GT21-08593_M_heart


title: DO278_ORSAM19526_GT21-08592_M_heart


title: DO285_ORSAM19533_GT21-08572_M_heart


title: DO275_ORSAM19523_GT21-08381_M_heart


title: DO276_ORSAM19524_GT21-08507_M_heart


title: DO274_ORSAM19522_GT21-08571_M_heart


title: AP1_blocked_dFosDN_42d_rep2


title: DO277_ORSAM19525_GT21-08523_M_heart


title: AP1_blocked_puc_42d_rep2


title: DO273_ORSAM19521_GT21-08395_M_heart


title: AP1_blocked_dFosDN_42d_rep1


title: AP1_blocked_puc_42d_rep1


title: DO272_ORSAM19520_GT21-08410_M_heart


title: DO271_ORSAM19519_GT21-08407_M_heart


title: dsRednegGFPneg_40d_rep4

value: dsRednegGFPneg


title: DO269_ORSAM19517_GT21-08394_F_heart

value: heart


title: DO270_ORSAM19518_GT21-08374_F_heart

value: 45% fat


title: DO268_ORSAM19516_GT21-08489_F_heart


title: dsRednegGFPneg_5d_rep4


title: AP1_blocked_ctrl_42d_rep1


title: DO267_ORSAM19515_GT21-08474_F_heart


title: DO287_ORSAM19535_GT21-08459_M_heart


title: DO266_ORSAM19514_GT21-08496_F_heart


title: dsRednegGFP+_40d_rep3

value: dsRednegGFP+


title: dsRednegGFP+_40d_rep4


title: dsRed+GFP+_40d_rep3

value: dsRed+GFP+


title: AP1_blocked_ctrl_42d_rep2


title: DO265_ORSAM19513_GT21-08497_F_heart


title: AP1_blocked_dFosDN_42d_rep3


title: dsRednegGFPneg_40d_rep3


title: dsRednegGFPneg_40d_rep2


title: DO264_ORSAM19512_GT21-08552_F_heart


title: DO262_ORSAM19510_GT21-08372_F_heart


title: dsRednegGFP+_40d_rep2


title: dsRed+GFP+_40d_rep2


title: dsRednegGFPneg_5d_rep3


title: DO261_ORSAM19509_GT21-08436_F_heart


title: DO260_ORSAM19508_GT21-08401_F_heart


title: dsRed+GFP+_40d_rep4


title: dsRednegGFPneg_5d_rep2


title: dsRednegGFPneg_40d_rep1


title: dsRednegGFP+_40d_rep1


title: DO258_ORSAM19506_GT21-08597_F_heart


title: dsRed+GFP+_40d_rep1


title: DO257_ORSAM19505_GT21-08630_F_heart


title: dsRednegGFPneg_5d_rep1


title: neuronal_ND42_RNAi_rep4


title: DO255_ORSAM19503_GT21-08454_F_heart


title: DO256_ORSAM19504_GT21-08623_F_heart


title: DO253_ORSAM19501_GT21-08520_F_heart


title: neuronal_ND42_RNAi_rep3


title: neuronal_mCherryRNAi_rep4

value: TREdsRed;elavGS>UAS-mCherry-RNAi


title: DO252_ORSAM19500_GT21-08366_F_heart


title: DO251_ORSAM19499_GT21-08498_F_heart


title: neuronal_ND30_RNAi_rep3


title: DO259_ORSAM19507_GT21-08386_F_heart


title: DO250_ORSAM19498_GT21-08411_F_heart


title: neuronal_mCherryRNAi_rep2


title: neuronal_ND42_RNAi_rep2


title: DO249_ORSAM19497_GT21-08491_F_heart


title: neuronal_ND30_RNAi_rep2


title: neuronal_mCherryRNAi_rep3


title: DO248_ORSAM19496_GT21-08641_F_heart


title: neuronal_ND30_RNAi_rep1


title: DO245_ORSAM19493_GT21-08531_F_heart


title: neuronal_ND42_RNAi_rep1


title: DO246_ORSAM19494_GT21-08538_F_heart


title: DO244_ORSAM19492_GT21-08607_F_heart


title: SuHw_LOF_ovaries_1_8st_rep2_Hi-C

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Hi-C data was processed using the HiCExplorer suite version 3.4.2. The paired‐end reads in FastQ format were separately mapped to the Drosophila genome assembly dm6 using Bowtie2 (Galaxy Version 2.4.2+galaxy0), with the following options: --sensitive-local  --reorder. The raw contact Hi-C matrices in .h5 format with the bins size of 4 kb were generated in hicBuildMatrix (Galaxy Version 3.4.2.0).
Assembly: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary files format and content: h5

extract_protocol:
For the in situ Hi-C experiments, ovaries were collected in PBS buffer (200 pairs per Hi-C), cross-linked with 1% of formaldehyde for 5 min and then incubated for 5 min with 125 mM Glycine. Then ovaries were washed with 1xPBS buffer for three times. The remaining in situ Hi-C protocol was performed as described previously (Rao et al (2014) Cell, 159:1665-1680).
Hi-C libraries were prepared for sequencing using standard Illumina protocols

value: Ovaries were dissected from females 15 hours after eclosion

value: su(Hw)v/E8  stock (a gift of A. Golovnin)


title: neuronal_mCherryRNAi_rep1


title: DO243_ORSAM19491_GT21-08589_F_heart


title: WT_ovaries_1_8st_rep2_Hi-C

value: Ovaries were dissected from females 15 hours after eclosion (containing egg chambers corresponding to 1-8 stages)

value: Oregon-R modENCODE (Bloomington stock 25211)

value: no treatment


title: DO263_ORSAM19511_GT21-08387_F_heart


title: DO241_ORSAM19489_GT21-08509_F_heart


title: DO242_ORSAM19490_GT21-08457_F_heart


title: Wing disc, HP1a-chromo, RNAseq, rep4

city: Chapel Hill

first: Alexis

last: Stutzman

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

description:
transposon.count.rda
protein.count.rda

data_processing:
To count transcripts mapping to transposons or protein coding genes, fastq files for each genotype were merged then adapters were trimmed using bbmap version 38.75 then reads were mapped to a transposon reference (Bergman lab, https://github.com/bergmanlab/drosophila-transposons) or the dm6 reference genome using STAR. The resulting bam files were then counted using featureCounts and the dm6 protein coding gene annotation from ENSEMBL or a transposon annotation. Read counts were normalized to read-depth and transcript length to calculate reads per kilobase of transcript, per million (RPKM), then plotted using ggplot2.
Assembly: dm6
Supplementary files format and content: A featureCounts r object is provided for reads mapping to transposons and protein coding genes.

source_name: wing disc

growth_protocol: Stocks were maintained on standard cornmeal food at 25˚C. HP1acontrol and HP1achromo larvae were cultured by establishing vials with ten w1118; Df(2L)BSC228/CyO, Tb, RFP virgin females and, to produce HP1acontrol, a single yw; +; + male, or a single w1118; HP1achromo/CyO, Tb, RFP male (Table S3). After three days, genomic DNA from sacrificed w1118; HP1achromo/CyO, Tb, RFP males was sequenced to confirm the genotype the HP1achromo allele, which exhibits occasional instability. The remaining females were flipped daily and non-tubby third larval instar wandering females were used for experiments.

extract_protocol:
8 female 3LW larvae were collected and washed in 1xPBST (0.1% Triton), then washed in water and flash frozen. Larvae were homogenized in 1ml Trizol Reagent (Invitrogen #15596026). Extracted RNA was purified using Zymo Direct-zol RNA Miniprep kit (#ZR2070).
Tecan Universal RNA-seq kit with custom AnyDeplete, Drosophila (#30185152) was used for library preparation. Libraries were sequenced on a NovaSeqS4 (paired-end x100bp).

value: wing disc


title: Wing disc, HP1a-chromo, RNAseq, rep3

description:
transposon.count.rda
protein.count.rda


title: DO254_ORSAM19502_GT21-08542_F_heart


title: Wing disc, HP1a-chromo, RNAseq, rep2

description:
transposon.count.rda
protein.count.rda


title: DO240_ORSAM19488_GT21-08500_F_heart


title: DO239_ORSAM19487_GT21-08529_F_heart


title: DO238_ORSAM19486_GT21-08576_F_heart


title: DO247_ORSAM19495_GT21-08370_F_heart


title: Wing disc, HP1a-chromo, RNAseq, rep1

description:
transposon.count.rda
protein.count.rda


title: DO236_ORSAM19484_GT21-08425_F_heart


title: Wing disc, HP1a-control, RNAseq, rep1

description:
transposon.count.rda
protein.count.rda


title: Wing disc, HP1a-control, RNAseq, rep3

description:
transposon.count.rda
protein.count.rda


title: SuHw_LOF_ovaries_1_8st_RNASeq_rep2

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
For ChIP-Seq data the single‐end reads in FastQ format were mapped to the Drosophila genome assembly dm6 using Bowtie2 (Galaxy Version 2.3.4.3) and filtered (with minimum MAPQ quality score = 5). BigWig files were generated using bamCoverage (Galaxy Version 3.5.1.0.0) with scores representing number of reads per kilobase per million (RPKM). The final BigWig files (representing the protein-binding profiles) were obtained using bigwigcompare (Galaxy Version 3.5.1.0.0) as a ratio of ChIP signal to Input.
For RNA-Seq data the paired-end reads were mapped to the Drosophila genome assembly dm6 using HISAT2 (Galaxy Version 2.2.1+galaxy0). BigWig files were generated using bamCoverage (Galaxy Version 3.3.2.0.0) with scores representing number of reads per kilobase per million (RPKM).
Hi-C data was processed using the HiCExplorer suite version 3.4.2. The paired‐end reads in FastQ format were separately mapped to the Drosophila genome assembly dm6 using Bowtie2 (Galaxy Version 2.4.2+galaxy0), with the following options: --sensitive-local  --reorder. The raw contact Hi-C matrices in .h5 format with the bins size of 4 kb were generated in hicBuildMatrix (Galaxy Version 3.4.2.0).
Assembly: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary files format and content: bigwig

extract_protocol:
For the ChIP-Seq experiments ovaries were collected in PBS buffer (50 pairs per ChIP), cross-linked with 1% of formaldehyde for 5 min and then incubated for 5 min with 125 mM Glycine. After that ovaries were washed with PBS buffer for three times. The remaining ChIP protocol was performed as described previously (Vorobyeva et al (2013) NAR, 41:11, 5717–5730). For the in situ Hi-C experiments, ovaries were collected in PBS buffer (200 pairs per Hi-C), cross-linked with 1% of formaldehyde for 5 min and then incubated for 5 min with 125 mM Glycine. Then ovaries were washed with 1xPBS buffer for three times. The remaining in situ Hi-C protocol was performed as described previously (Rao et al (2014) Cell, 159:1665-1680). For extraction of RNA the ovaries of 15 hour old wild-type (oregon) and su(Hw)v/E8 females were collected in PBS buffer (50 pairs per sample), in two biological repeats. Total RNA was extracted with the TRI reagent (Ambion). PolyA comprising RNA fraction was isolated and prepared for sequencing with the NEBNext UltraTM II Directional RNA Library Prep Kit.
ChIP-Seq, Hi-C and RNA-Seq libraries were prepared for sequencing using standard Illumina protocols


title: Wing disc, HP1a-control, RNAseq, rep2

description:
transposon.count.rda
protein.count.rda


title: DO234_ORSAM19482_GT21-08493_F_heart


title: DO233_ORSAM19481_GT21-08502_F_heart


title: WT_ovaries_1_8st_RNASeq_rep2


title: DO231_ORSAM19479_GT21-08590_F_heart


title: neuronal_ND30_RNAi_rep4

value: RU-486 continuous, 29C


title: DO229_ORSAM19477_GT21-08519_F_heart


title: DO228_ORSAM19476_GT21-08486_F_heart


title: SuHw_LOF_ovaries_1_8st_ChIP_Paf1

value: anti-Paf1 antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189)


title: SuHw_LOF_ovaries_1_8st_ChIP_Rpb3

value: anti-Rpb3 antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189)


title: DO227_ORSAM19475_GT21-08541_F_heart


title: SuHw_LOF_ovaries_1_8st_ChIP_NELF_E

value: anti-NELF E antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189)


title: SuHw_LOF_ovaries_1_8st_ChIP_Combgap

value: anti-Combgap antibodies (Chetverina et al (2022) Cell Mol Life Sci, 79(7):353)


title: DO226_ORSAM19474_GT21-08631_F_heart


title: DO225_ORSAM19473_GT21-08501_F_heart


title: DO224_ORSAM19472_GT21-08582_F_heart


title: DO237_ORSAM19485_GT21-08476_F_heart


title: WT_ovaries_1_8st_ChIP_Rpb3


title: WT_ovaries_1_8st_ChIP_Paf1


title: WT_ovaries_1_8st_ChIP_NELF_E


title: DO223_ORSAM19471_GT21-08595_F_heart


title: WT_ovaries_1_8st_ChIP_Combgap


title: DO222_ORSAM19470_GT21-08383_F_heart


title: SuHw_LOF_ovaries_1_8st_RNASeq_rep1


title: IgG rep2

first: Bjoern

last: von Eyss

address: Beutenbergstr. 11

institute: Leibniz Institute on Aging

data_processing:
FASTQ files were processed by the cellranger pipeline using default settings.
Assembly: mm10
Library strategy: CUT&Run

source_name: luminal cell (mammary gland)

extract_protocol:
Mammary gland tissue was dissociated using gentle collagenase/hyaluronidase (Stemcell), mammary epithelial cells were further isolated using 0,25 % trypsin (Gibco) and 5 mg/mL dispase  (Merck). Mammary epithelial luminal cells were sorted via FACS using EpCAM and CD49f surface markers (antibodies:  12-9326-42 from eBioscience and 313631 from Biolegend). For each CUT and RUN reaction, 200,000 cells were bound to activated concanavin A magnetic beads (Polysciences) and incubated with the desired antibody (1:100) in the presence of 0.01 % digitonine. DNA was cleaved using 1 μg/mL protein A/G Micrococcal Nuclease fusion protein (pA/G MNase) in the presence of 0.01% digitonine. Samples were treated with RNAse and Protreinase K and the released DNA was purified using Phenol/Chloroform/Isoamyl alcohol
DNA library generation with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s recommendations. Adaptor ligation was performed with 1:25 diluted adaptor and 15 cycles were used for library amplification.

treatment_protocol: Cells isolated from wild type animals

value: luminal cell (mammary gland)

value: wild type

tag: cut&run antibody

value: IgG (Sigma:I5006 Sigma-Aldrich)


title: DO232_ORSAM19480_GT21-08613_F_heart

tag: tissue

value: heart

value: 45% fat


title: WT_ovaries_1_8st_RNASeq_rep1

tag: genotype


title: DO220_ORSAM19468_GT21-08376_M_heart


title: DO219_ORSAM19467_GT21-08422_M_heart


title: DO221_ORSAM19469_GT21-08429_F_heart


title: DO230_ORSAM19478_GT21-08585_F_heart


title: IgG rep1


title: SuHw_LOF_ovaries_1_8st_rep1_Hi-C

tag: treatment


title: WT_ovaries_1_8st_rep1_Hi-C


title: DO235_ORSAM19483_GT21-08481_F_heart


title: DO218_ORSAM19466_GT21-08516_M_heart


title: DO217_ORSAM19465_GT21-08601_M_heart


title: TRPS1 rep1

value: TRPS1 (Abcam:ab209664)


title: shTRPS1 EtOH

library_source: genomic single cell

data_processing:
FASTQ files were processed by the cellranger pipeline using default settings.
Assembly: mm10

source_name: primary mouse organoid

growth_protocol: Mammary organoids were cultured with matrigel in organoid medium (DMEM/F12 + Glutamax with addition of 1X N-2 Supplement, 1X B27 Supplement, 100 ng/mL Neuregulin, 100 ng/mL Noggin and 100 ng/mL R-spondin)

extract_protocol:
Orgnaoids were dissociated in TrypLE Express Enzyme (ThermoFisher Scientific). Nuclei were isolated by lysing the cells with chilled lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 0.1%Nonidet P40, 0.01 % Digitonin, 1 % BSA) on ice for 3 min 30 s. Cells were washed with wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 1 % BSA). Supernatant was discarded and cells were resuspended in 1X Nuclei Buffer (10X Genomics, PN-2000153/ 2000207). 7600 nuclei were loaded onto the Chroimium Controller to recover 5000 nuclei for library prepration and sequencing.
10x Genomics Chromium Controller and Chromium Next GEM Single Cell ATAC Reagent Kits v2 according to the manufacturer’s protocol (CG000496)

treatment_protocol: Mammary organoids isolated from shTrps1-expressing mice were treated with Doxycycline (0,1 µg/mL) or Ethanol as control for 7 days.

value: primary mouse organoid

value: shTRPS1.34 ki/+; CAG-rtTA3 tg/+

value: EtOH


title: DO216_ORSAM19464_GT21-08379_M_heart


title: shTRPS1 DOX

value: doxycycline (0.1 ug/ml)


title: shTRPS1.32_rep2_ADT

source_name: mammary gland

extract_protocol:
Mammary gland tissue was dissociated using gentle collagenase/hyaluronidase (Stemcell), mammary epithelial cells were further isolated using 0.25% trypsin  (Gibco) and 5 mg/mL dispase (Stemcell) treatments. Cells were incubated with 0.5 µg of TotalSeq antibodies (anti-EpCAM, anti-CD49f, 118237 and 313633 from Biolegend)
10x Genomics scRNA-Seq was performed using the Chromium single cell 3’ assay v3 as recommended by the manufacturer.

treatment_protocol: Mice were given doxycycline supplemented food (625 mg/kg, ssniff) for 10 days to induce the expression of the shRNA (shTrps1.32/shTrps1.34 or shRenilla control depending on the animal genotype).

value: mammary gland

value: shTRPS1.32 ki/+; CAG-rtTA3 tg/+

tag: cell type

value: EpCAM-enriched cells


title: DO214_ORSAM19462_GT21-08549_M_heart


title: DO213_ORSAM19461_GT21-08475_M_heart


title: shTRPS1.32_rep1_ADT


title: shRen_rep3_ADT

value: shRen ki/+; CAG-rtTA3 tg/+


title: DO212_ORSAM19460_GT21-08608_M_heart


title: TRPS1 rep2


title: DO211_ORSAM19459_GT21-08467_M_heart


title: shRen_rep1_ADT


title: shTRPS1.34_rep1_ADT


title: shRen_rep2_ADT


title: DO209_ORSAM19457_GT21-08643_M_heart


title: DO207_ORSAM19455_GT21-08568_M_heart


title: DO208_ORSAM19456_GT21-08525_M_heart


title: DO206_ORSAM19454_GT21-08554_M_heart


title: shTRPS1.32_rep2_GEX


title: DO205_ORSAM19453_GT21-08412_M_heart


title: shTRPS1.34_rep1_GEX


title: DO210_ORSAM19458_GT21-08517_M_heart


title: shRen_rep2_GEX


title: shRen_rep1_GEX


title: shRen_rep3_GEX


title: DO215_ORSAM19463_GT21-08365_M_heart


title: DO204_ORSAM19452_GT21-08539_M_heart


title: DO202_ORSAM19450_GT21-08574_M_heart